Metabolic Pathways of Leishmania Parasite: Source of Pertinent Drug Targets and Potent Drug Candidates

Leishmania donovani homoserine dehydrogenase: Biochemical and structural characterization of a novel parasite specific enzyme of aspartate pathway

Visceral leishmaniasis is a neglected tropical disease. Drug resistance and toxicity are the critical issues with the currently available antileishmanial drugs. Therefore, research efforts are underway to identify and validate new drug targets specific to Leishmania parasite. The enzyme homoserine dehydrogenase (HSD) functions in the third step of aspartate pathway. The present study focuses on the biophysical and biochemical characterization of HSD enzyme from Leishmania donovani (LdHSD) which is unique to the parasite with no homologous enzyme in the host. LdHSD gene was cloned in pET28c(+) vector and transformed in E. coli BL21 (DE3) strain. LdHSD recombinant enzyme of molecular weight 46.6 kDa with 6X-His tag at the C-terminal end was expressed, purified by nickel affinity chromatography and confirmed by western blot analysis using anti-His antibody. Effect of pH, temperature, salts, metal ions and amino acids on the recombinant enzyme were evaluated. Kinetic parameters of LdHSD were evaluated for substrates L-homoserine and NADP+. Biophysical analysis revealed that the enzyme is rich in β-sheets. Thermal denaturation study revealed that the protein is stable up to 45 °C. Furthermore, comprehensive comparative sequence analysis and structural modeling revealed the structural and functionally important residues, which are involved in the catalytic mechanisms. The putative binding mode of the natural substrate L-homoserine into the active site of LdHSD was also elucidated. These findings provide a foundation for the development of selective, target-based inhibitors against the HSD enzyme of the parasite.

Identification of putative volatile biomarkers of canine leishmaniasis in dog's breath and hair employing a novel algorithm for automated chromatographic peak detection and matching

The analysis of the volatile compounds released by biological samples represents a promising approach for the non-invasive diagnosis of a disease. The present study, focused on a population of dogs infected with canine leishmaniasis, aimed to decipher the volatolomic profile associated with this disease in dogs, which represent the main animal reservoir for Leishmania pathogen transmission to humans. The volatiles emitted by the breath and hair of dogs were analysed employing the gas chromatography-mass spectrometry (GC-MS) technique. The acquired chromatograms were investigated using a novel algorithm developed in this study for automated chromatographic peak detection and matching in untargeted GC-MS analysis, which includes various steps that comprise noise reduction, m/z filtering, background subtraction, peak detection, peak matching, and generation of a peak table for compounds identification. The results revealed one tentative breath volatile biomarker and five tentative hair volatile biomarkers for the cutaneous form of the disease, which is characterised by skin ulcerations. Additionally, nine tentative breath volatile biomarkers and four tentative hair volatile biomarkers were found for the visceral form of the disease, which affects internal organs such as spleen, liver and bone marrow. All tentative biomarkers identified in this study were upregulated in cutaneous leishmaniasis, while in visceral leishmaniasis, all tentative biomarkers were upregulated in the breath and only one out of four in the hair. Only one compound (glyceryl monooleate) was identified as tentative volatile biomarker for both forms of the disease, in the hair of dogs.

Exploring glycolytic enzymes in disease: potential biomarkers and therapeutic targets in neurodegeneration, cancer and parasitic infections

Glycolysis, present in most organisms, is evolutionarily one of the oldest metabolic pathways. It has great relevance at a physiological level because it is responsible for generating ATP in the cell through the conversion of glucose into pyruvate and reducing nicotinamide adenine dinucleotide (NADH) (that may be fed into the electron chain in the mitochondria to produce additional ATP by oxidative phosphorylation), as well as for producing intermediates that can serve as substrates for other metabolic processes. Glycolysis takes place through 10 consecutive chemical reactions, each of which is catalysed by a specific enzyme. Although energy transduction by glucose metabolism is the main function of this pathway, involvement in virulence, growth, pathogen-host interactions, immunomodulation and adaptation to environmental conditions are other functions attributed to this metabolic pathway. In humans, where glycolysis occurs mainly in the cytosol, the mislocalization of some glycolytic enzymes in various other subcellular locations, as well as alterations in their expression and regulation, has been associated with the development and progression of various diseases. In this review, we describe the role of glycolytic enzymes in the pathogenesis of diseases of clinical interest. In addition, the potential role of these enzymes as targets for drug development and their potential for use as diagnostic and prognostic markers of some pathologies are also discussed.

Structure-based Virtual Screening and Drug Design Development of Leishmanicidal Pyrimidines

Leishmaniasis is a neglected disease caused by parasites of the genus Leishmania sp. that causes approximately 1 million cases and 650,000 deaths annually worldwide. Its treatment has several limitations mainly due to high toxicity and clinical resistance, and the search for alternatives is highly desirable. The present work aimed to design new antileishmanial compounds through a virtual screening of a small in-house library of pyrimidine compounds, never tested against Leishmania, using the active site of trypanothione reductase (TR) as a target model. The compounds showed favorable affinity with the amino acid residues of the active site of TR. Pyr 1-9 were synthesized and tested against Leishmania amazonensis strain. Four derivatives demonstrated activity against promastigote (IC50 value between 11.23 and 91.5 µM) and three other compounds demonstrated discreet activity against amastigote, IC50 value between 81.29 and 153.21 µM. Based on the results obtained in the screening, three new pyrimidines Pyr 10-12 were designed to optimize activity, cytotoxicity, and selectivity. Pyr 10 and Pyr 11 demonstrated good activity against promastigotes, with IC50 of 11.38 ± 9.7 and 20.01 ± 13.55 µM, respectively, and improved cytotoxicity and selectivity. No activity was obtained against amastigotes. Thus, this study contributes important information for the development of new pyrimidines active against Leishmania.

Hit-to-lead optimization of 4,5-dihydrofuran-3-sulfonyl scaffold against Leishmania amazonensis. Effect of an aliphatic moiety

In line with our objective of designing new antileishmanial compounds for oral use, we report the synthesis and biological evaluation in vitro of original 4,5-dihydrofuran derivatives bearing an amidoxime group. Previous optimization focused on position 3 of the dihydrofuran ring involving aromatic fragments, resulting in the identification of the compound (HIT) 4-(5-benzyl-3-((4-fluorophenyl)sulfonyl)-5-methyl-4,5-dihydrofuran-2-yl)-N'-hydroxybenzimidamide (IC50 = 5.4 ± 1.0 μM, L. amazonensis promastigote, IC50 = 7.9 ± 1.1 μM, L. amazonensis intracellular amastigote). In the present work, position 3 was substituted with an aliphatic moiety. This modification was guided by a ligand-based approach, given the unknown biological target or mechanism of action for this compound. The 4,5-dihydrofuran derivatives were synthesized using microwave-assisted manganese (III) acetate-based oxidative cyclization of linear β-keto-carboxylic and β-keto-sulfone substrates, overcoming synthetic challenges to obtain aliphatic derivatives of 4,5-dihydrofuran-3-carboxamides. Finally, an unexpected and interesting biological activity with the 4,5-dihydrofuran-3-carboxylate (IC50 < 5 μM) against the amastigote form is discussed.

Harnessing computational and experimental approaches to identify potent hits against Leishmania donovani sterol C-24 methyltransferase from ChemBridge library

Leishmaniasis is a neglected tropical disease and is one of the major causes of mortality in poverty-stricken areas. A limited chemotherapeutics arsenal is available to tackle this deadly infection. Thus, identifying novel potent scaffolds using innovative strategies is the need of the hour. High-throughput screening (HTS) is a critical technique that can accelerate the process of drug discovery by evaluating millions of drug-like molecules using various automation tools and biological assays. In the present study, we have employed the HTS strategy to identify potent hits against Leishmania donovani sterol C-24 methyltransferase (LdSMT) from the in-house ChemBridge library. Firstly, a robust dataset was prepared with previously reported sterol C-24 methyltransferase inhibitors, belonging to diverse structural classes. Then, ligand-based virtual screening using similarity search was performed to screen the ChemBridge library having ∼20,000 molecules. This computational approach yielded 81 candidate compounds, which were selected for further molecular docking and biological evaluation. Anti-leishmanial assays revealed that out of 81 molecules, seven showed potential parasitic killing. Three molecules namely IIIM-CB-14, IIIM-CB-29, and IIIM-CB-45 were the most potent ones with 50 % inhibitory concentration (IC50) of 5.76, 8.08, and 10.64 µg/mL, respectively. SEM analyses suggest that these potent hits cause considerable morphological alterations. ADME studies of the potent hit molecules indicate that all the hits have considerable drug-likeness properties. Further, molecular dynamics studies were also performed to check the stable confirmation of LdSMT protein with the top two hits (IIIM-CB-14 and IIIM-CB-45). Thus, the present study harnesses computational and experimental approaches to unravel potent anti-leishmanial scaffolds.

Possibility of re-purposing antifungal drugs posaconazole & isavuconazole against promastigote form of Leishmania major

Background & objectives The emergence of drug resistance in leishmaniasis has remained a concern. Even new drugs have been found to be less effective within a few years of their use. Coupled with their related side effects and cost-effectiveness, this has prompted the search for alternative therapeutic options. In this study, the Computer Aided Drug Design (CADD) approach was used to repurpose already existing drugs against Leishmania major. The enzyme lanosterol 14-alpha demethylase (CYP51), in L. major, was chosen as the drug target since it is a key enzyme involved in synthesizing ergosterol, a crucial component of the cell membrane. Methods A library of 1615 FDA-approved drugs was virtually screened and docked with modeled CYP51 at its predicted binding site. The drugs with high scores and high affinity were subjected to Molecular Dynamics (MD) simulations for 100 ns. Finally, the compounds were tested in vitro using an MTT [3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide] assay against the promastigotes of L. major. Results Computational screening of FDA-approved drugs identified posaconazole and isavuconazole as promising candidates, as both drugs target the CYP51 enzyme in fungi. Molecular dynamics (MD) simulations demonstrated that both drugs form stable complexes with the target enzyme. In vitro studies of posaconazole and isavuconazole against promastigotes of L. major demonstrated significant efficacy, with IC50 values of 2.062±0.89 µg/ml and 1.202±0.47 µg/ml, respectively. Interpretation & conclusions The study showed that the existing FDA-approved drugs posaconazole and isavuconazole can successfully be repurposed for treating L. major by targeting the CYP51 enzyme, demonstrating significant efficacy against promastigotes.

Identification of new potential inhibitors of pteridine reductase-1 (PTR1) via biophysical and biochemical mechanism-based approaches: Step towards the treatment of Leishmaniasis

Leishmaniasis is a parasitic disease, which spreads from the bite of an infected Phlebotomine fly to human hosts. The disease is characterized by a number of clinical manifestations, such as ulcerative lesions at the site of sandfly bite (cutaneous form), inflammation of mucosal membranes (mucosal leishmaniasis) or the deadly visceral form. This study was aimed to target pteridine reductase-1 (PTR1), a member of short chain dehydrogenases, which accounts for the reduction of conjugated and unconjugated pterins in Leishmania parasite. The ptr1-pET28a+-tev construct was expressed using BL21 (DE3) cells, followed by two tandem purification steps including affinity and gel permeation chromatography. In the next phase, functional studies of PTR1 were performed via screening of an in-house library of 500 compounds. The biochemical-mechanism based assay of PTR1 identified 11 hits that were also found to be non-cytotoxic against human fibroblast cell line (BJ) (except compound 6), and thus further studied via computational technique and saturation transfer difference-nuclear magnetic resonance (STD-NMR) spectroscopy. These high throughput techniques identified six compounds 2, 4, 5, 7, 9, and 11 as active, which were then assessed via in-vitro assay. Among them, compounds 2, 4, and 7 showed substantial leishmanicidal activity, comparable to the standard drug, miltefosine (IC50 value: 31.8 ± 0.2 μM). These results narrowed down the search to 3 compounds as potential leads, with prominent protein-ligand interaction profiles. Hence, the respective compounds can be further assessed for their therapeutic potential against leishmaniasis.

Repurposing FDA approved drugs against Sterol C-24 methyltransferase of Leishmania donovani: A dual in silico and in vitro approach

Leishmaniasis is a disease caused by the parasite Leishmania donovani affecting populations belonging to developing countries. The present study explores drug repurposing as an innovative strategy to identify new uses for approved clinical drugs, reducing the time and cost required for drug discovery. The three-dimensional structure of Leishmania donovani Sterol C-24 methyltransferase (LdSMT) was modeled and 1615 FDA-approved drugs from the ZINC database were computationally screened to identify the potent leads. Fulvestrant, docetaxel, indocyanine green, and iohexol were shortlisted as potential leads with the highest binding affinity and fitness scores for the concerned pathogenic receptor. Molecular dynamic simulation studies showed that the macromolecular complexes of indocyanine green and iohexol with LdSMT remained stable throughout the simulation and can be further evaluated experimentally for developing an effective drug. The proposed leads have further demonstrated promising safety profiles during cytotoxicity analysis on the J774.A1 macrophage cell line. Mechanistic analysis with these two drugs also revealed significant morphological alterations in the parasite, along with reduced intracellular parasitic load. Overall, this study demonstrates the potential of drug repurposing in identifying new treatments for leishmaniasis and other diseases affecting developing countries, highlighting the importance of considering approved clinical drugs for new applications.

A review on potential therapeutic targets for the treatment of leishmaniasis

Leishmania, a protozoan parasite, is responsible for the occurrence of leishmaniasis, a disease that is prevalent in tropical regions. Visceral Leishmaniasis (VL), also known as kala-azar in Asian countries, is one of the most significant forms of VL, along with Cutaneous Leishmaniasis (CL) and Mucocutaneous Leishmaniasis (ML). Management of this condition typically entails the use of chemotherapy as the sole therapeutic option. The current treatments for leishmaniasis present several drawbacks, including a multitude of side effects, prolonged treatment duration, disparate efficacy across different regions, and the emergence of resistance. To address this urgent need, it is imperative to identify alternative treatments that are both safer and more effective. The identification of appropriate pharmacological targets in conjunction with biological pathways constitutes the initial stage of drug discovery. In this review, we have addressed the key metabolic pathways that represent potential pharmacological targets as well as prominent treatment options for leishmaniasis.

Repurposing of Food and Drug Admnistration (FDA) approved library to identify a potential inhibitor of trypanothione synthetase for developing an antileishmanial agent

Leishmaniasis is one of the top 10 neglected tropical diseases. Globally, it impacts more than 12 million individuals. In light of the absence of a safer, affordable treatment for the Leishmaniasis, along with therapeutic failures and drug resistance, novel therapeutic strategies are necessary to discover new drugs. Treatment would benefit by concentrating on the precise targets that are crucial for the parasite to survive. A target that aids in the organism's survival under oxidative stress is trypanothione synthetase (TyS), which is a component of the trypanothione pathway in Leishmania spp. To find potential TyS inhibitors for the purpose of discovering novel antileishmanial drugs, we used a virtual screening strategy. Using the Glide module of Schrodinger-suite 2023, an FDA-approved library containing 2000 drugs from the ZINC-15 database was screened against the TyS. Dostinex, raloxifene, and formoterol showed good docking scores of -10.568 kcal/mol, -10.446 kcal/mol, and -56.21 kcal/mol, as well as good binding energies of -70.41 kcal/mol, -56.21 kcal/mol, and -64.15 kcal/mol respectively. The stability of the ligand-protein complexes was assessed further with the help of Desmond to execute a 100-ns molecular dynamics simulation. The Prime module was utilised to perform post-MM/GBSA analysis on these three molecules along with the toxicity profiling using Protox II web server. This study suggests that dostinex, formoterol, and raloxifene may act as effective inhibitors of the TyS receptor which could be used as novel antileishmanial agents for the therapeutic applications. Thorough preclinical studies are necessary to confirm the identified compounds chemotherapeutic qualities.

GSK-3 kinase a putative therapeutic target in trypanosomatid parasites

Trypanosomatids are an important group of parasites that predominate in tropical and subtropical areas of the planet, which cause diseases that are classified as forgotten and neglected by the world health organization. In this group of parasites, we find Trypanosoma cruzi, Trypanosoma brucei, Trypanosoma brucei rhodesiense and Leishmania spp, for which there is no vaccine available, and its control has focused mainly on pharmacological treatment. Due to the poverty situation where these diseases are found and the biological complexity of these parasites, there are multiple variables to control, including the diversity of species, the complexity of their life cycles, drug resistance, cytotoxicity, the limited use in pregnant women, the high costs of treatment and the little-known pharmacological mechanisms of action, among others. It is therefore necessary to find new strategies and approaches for the treatment of these parasitic diseases. Among these new approaches is the rational search for new targets based on the allosteric inhibition of protein kinases, which have been little studied in trypanosomatids. Among these kinases, we find Glycogen Synthase Kinase-3 (GSK-3), a kinase of great pharmacological interest, which is under intense basic and clinical research by pharmaceutical companies for the treatment of cancer. This kinase, highly studied in the PI3K/AKT/mTOR pathway signaling in humans, has an orthologous gene in these parasites (GSK-3 s), which has proven to be essential for them in response to different challenges; Therefore, it is notable to increase research in this kinase in order to achieve a broad structural and functional characterization in the different species of trypanosomatids.

Photodynamic therapy mediated by a red LED and methylene blue inactivates resistant Leishmania amazonensis

Cutaneous leishmaniasis is a neglected parasitic disease that leads to destructive lesions. The emergence of drug resistance has been a global concern over the past years. Photodynamic therapy (PDT) mediated by a red LED and methylene blue (MB) involves the overproduction of oxidative stress, which oxidizes several cellular biomolecules and prevents the selection of resistant strains. Herein, we investigated the potential of PDT mediated by MB against wild-type and miltefosine-resistant strains of Leishmania amazonensis. As a result, both strains were susceptible to PDT, thus encouraging us to seek the best conditions to overcome the drug resistance problem in cutaneous leishmaniasis.

Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets

Amid emerging drug resistance to metal inhibitors, high toxicity, and onerous drug delivery procedures, the computational design of alternate formulations encompassing functional metal-containing compounds greatly relies on large-scale atomistic simulations. Simulations particularly with Au(I), Ag, Bi(V), and Sb(V) pose a major challenge to elucidate their molecular mechanism due to the absence of force field parameters. This study thus quantum mechanically derives force field parameters of Bi(V) as an extension of the previous experimental study conducted on heteroleptic triorganobismuth(V) biscarboxylates of type [BiR3(O2CR')2]. We have modeled two organo-bismuth(V) carboxylates, which are optimized and parameterized along with the famous pentavalent antimonial drug: meglumine antimoniate using quantum mechanics original Seminarian methods with the SBKJC effective core potential (ECP) basis set. Furthermore, molecular dynamics (MD) simulations of bismuth- and antimony-containing compounds in complex with two enzymes, trypanothione synthetase-amidase (TSA) and trypanothione reductase, are performed to target the (T(SH)2) pathway at multiple points. MD simulations provide novel insights into the binding mechanism of TSA and highlight the role of a single residue Arg569 in modulating the ligand dynamics. Moreover, the presence of an ortho group in a ligand is emphasized to facilitate interactions between Arg569 and the active site residue Arg313 for higher inhibitory activity of TSA. This preliminary generation of parameters specific to bismuth validated by simulations in replica will become a preamble of future computational and experimental research work to open avenues for newer and suitable drug targets.